Attorney-General Yvette D'Ath says the allegations against Mr van der Merwe, while serious, do not suggest inappropriate interference with elections.
"This is pending a show cause notice as a consequence of serious allegations that have been brought to my attention which could amount to misbehaviour under Section 25 of the Electoral Act 1992," she said.
Ms D'Ath told reporters she had became aware of the allegations on Thursday afternoon and requested a special executive council meeting be convened on Monday.
"The details of the show cause process will be provided shortly to him, but he has been advised today, after approved by governor and council, that he is suspended and that there will be a show cause process," she said.
"I will be providing the electoral commissioner with the allegations and giving him adequate time to respond to those allegations before making a final decision."
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Educated in Zimbabwe and South Africa, Mr van der Merwe joined the Electoral Commission Queensland in 2010 as the assistant electoral commissioner and was appointed to the top job by the Newman government in 2014.
He was criticised in a state government report into the ECQ's handling of the 2016 local government elections which has been the focus of a Queensland Crime and Corruption Commission investigation.
The Ipswich, Logan, Gold Coast and Moreton Bay councils were all investigated over a number of matters, most particularly property developer donations.
Ms D'Ath said she wouldn't make any further comment until a state government misconduct investigation runs its course.
